Missing Legends
by BlairFalconeri
Summary: The legends have disappeared from their world and reappeared in Naruto's world. Now there's a potential threat in the Hidden Leaf. Are these kids friend of foe? Possible Title Change
1. Disappearances & Reappearances

**Chapter 1: Disappearances & Reappearances **

Red lights flashed along the empty hallway, the only sound was that of a set of running feet. The girl's hair flew wildly behind her as she raced toward the last door on the left. Throwing the door open, she glanced at the boy in front of the computer.

"Where are they," she asked, brushing her hair from her face and attempting to catch her breath.

"They're not in any of the other regions, I can tell you that," the boy said, turning from the screen to face his friend.

"What do you mean?"

"I mean," the boy said, fixing his hat, "the legendary Pokémon aren't in any of the regions. They've gone to a different dimension."

"You've gotta be fuc-"

"No I'm not. They aren't anywhere to be found."

The girl paused and looked at the boy in front of her. The boy noticed a look of hopelessness in his friend's grey eyes before she decided to speak again.

"Then what do we do?"

The boy smirked, "what else? We call the others and then follow the legendary Pokémon."

**Meanwhile – in Konoha**

It was a generally calm afternoon for the Village Hidden in the Leaves. Many shinobi were either relaxing in their homes or wandering through the streets. Our favorite shinobi were in their respective houses. Everything was calm until a loud crash shook the entire village.

Looking out their windows, people across the village attempted to figure out the cause of the explosion. Before their very eyes, a massive black and red bird appeared out of the smoke near the gates. Civilians began to panic while experienced shinobi prepared to defend the village.

Within the Hokage tower, Tsunade shouted for Shizune to send out as many shinobi as they could to call for an evacuation of the civilians as well as those shinobi that could not fight.

As shinobi moved in on the bird-like creature, they noticed another creature. This one resembled a large, blue stag, which caused the shinobi from the Nara clan to take a second glance at the new creature.

Some of the first shinobi that reached the creatures started to attack, the voice of a girl echoed through the surrounding area. "Sekhmet, don't let them hurt Yveltal or Xerneas!"

A white, dog-like creature with a black crescent appearing through the fur jumped between the shinobi and the two larger creatures, a fierce look plastered on its face.

"Sekhmet, use dark pulse of Yveltal!"

The white furred creature turned to face the bird before jumping into the air and releasing a wave of dark colored energy toward the bird. Dodging the attack, the bird, now known to the shinobi as Yveltal, charged toward the much smaller creature.

"Greninja, use smokescreen," a male voice shouted. By this time, the shinobi had stopped their attack, unsure of how to proceed in the current situation.

A blue frog flew toward the Yveltal before releasing a cloud of smoke at the much larger creature, giving the two smaller ones an opportunity to move out of Yveltal's way. The stag's eyes grew wide before it started to back away into the forest.

"Shit," the girl swore under her breath, "Sekhmet, use sucker punch!"

But it was too late. The stag had already disappeared into the forest. Swearing again, the girl turned to her partner, "Xerneas got away!"

"Then we'll have to find Xerneas later! Focus on Yveltal!"

Nodding, the girl turned to the white, dog-like creature by her side, "use bite, Sekhmet!"

Leaping toward the bird with jaws open, Yveltal knocked the smaller creature away and into a tree before turning toward the sky to retreat. The girl gasped, rushing over to the creature to check her wounds. This time, the boy swore and turned to the blue frog by his side. "Greninja, hit him with water shuriken!"

However, just like Xerneas, Yveltal had disappeared into the night sky. "He's gone," the boy called out to the girl. The girl petted her furred creature before taking out a black and yellow ball. Hitting the button in the center, the ball opened and turned the creature into light before it disappeared into the ball. The boy did the same thing to his frog as the girl walked over to join him.

"What do we do now," she asked, placing the now smaller ball into her bag.

The boy rubbed his face before pinching the bridge of his nose. "I have no idea. I guess we'll have to track them before someone else does."

"I'm sorry, but you'll have to come with us for questioning."

The duo turned to find a white haired man standing in front of them. Looking him up and down, the girl put a hand on her hip. "I don't think so, bud."

"I'm sorry, but with such powerful creatures at your disposal, you are a risk to the village until we have our questions answered. Now, if you could come with us, then we can release you quicker."

Other shinobi started to take a step closer in case the two tried to run.

"We aren't going with you," the boy said, "we have more important things to do."

"Then I guess we have to choice," the white haired man said. Hands reached for the bags that the two had and, despite their efforts, the shinobi confiscated the bags and grabbed hold of the potential threats, teleporting the two away for their interrogations.

**This is just something that came to mind as I was working on my Pokémon/Harry Potter crossover. If you would like me to continue this story, please leave a comment! Thank you for reading! :)**

**So that there's no confusion, Sekhmet is an Absol.**


	2. Babysitters

**Chapter 2: Babysitters**

"If anything happens to my Pokémon, I swear to Arceus-"

"So that's what those creatures are called," a man with broad shoulders asked. The girl looked toward him, immediately noticing the two scars that crossed his face.

"Why would I tell you that," she spat.

The man raised an eyebrow, "these aren't difficult questions. If you cooperate, then you can have them back sooner."

The girl paused for a moment before speaking, "you've kept me here all night without any explanation, tie me to a chair, _and_ you're keeping my Pokémon away from me. What makes you think that I'm going to cooperate?"

The man simply stood in front of her, no emotions visible on his face. She sighed in exasperation before speaking again, "for the love of Arceus. My name is Serena Fortier. I'm 15 years old, and I need my Pokémon back so I can leave and actually finish this job."

The man only looked at her, writing down the girl's name and age. "Why were those creatures so close to the village?"

"How am I supposed to know," Serena snapped, "I don't have any control over where they go. We just followed them."

"You and your friend, that boy?"

"No, my imaginary friend Mr. Fluffy," she replied blandly, "yes, I mean the boy."

"I'm just trying to determine if you and your friend are a threat to the village."

"I've been told that a thousand times already! He and I are not a threat, our Pokémon aren't a threat. Can we go know?"

Before the man could answer, the door to the room opened. Another man poked his head in, gesturing for Serena's interrogator to go over to the door. The interrogator went to the door and spoke to the new man for a few minutes. The door soon closed and the interrogator walked back over to the chair that Serena had been. He began to untie Serena and pulled her up from the chair. "Well, it seems like your friend was more help than you were."

"What did you do to him," she hissed.

"We didn't do anything to him. He was actually much calmer than you were."

Before Serena could even respond, the duo disappeared, only to reappear in an office. Serena looked around the room, noticing a blonde woman behind a desk, a younger, dark haired woman beside her, and standing in front of the woman was her dark haired friend.

"Calem," Serena said quietly before moving toward him, wrapping her arms around his shoulders. "What happened, did they hurt you?"

Calem smiled, wrapping his arms around Serena, "I'm fine, Serena. They didn't do anything to me."

The blonde woman cleared her throat, causing the friends to break apart and face the woman. "So," she began, "those creatures that were fighting last night are called Pokémon, correct?"

"Yes ma'am," Calem said calmly.

"The larger ones are known as Xerneas and Yveltal, while the smaller ones are Greninja and Sekhmet."

"The first three are correct," Serena said, "my Sekhmet is actually an Absol. Sekhmet's just the name I gave her."

The blonde woman looked up from the paper she was reading. She glanced between the two of us for a moment before looking back down at the paper I her hands. "For the time being, you each will be staying with one of the clans for further observation."

"You can't do that," Serena hissed, "we don't have time so sit around and wait for you to decide if we're a treat! Calem and I need to leave now! We can't afford to have someone else find those Pokémon before we do!"

"You will have plenty of time to explain the situation in front of the council meeting tomorrow." The blonde woman then turned to her younger assistant, "Shizune, send for representatives from the Aburame and Akimichi clans." The young woman then left, giving her boss a nod before walking toward the door.

_Great,_ Serena thought, _under house arrest in someone else's house. This is starting to sound more like babysitting._

Within ten minutes, the woman returned, this time with four people. The first was a heavy set, middle-aged man with purple markings on is cheeks, followed by a boy, most likely the first man's son. The next duo that walked into the room were almost completely covered, except for half of their faces. However, their eyes were covered by sunglasses.

"Were these the two that were found at the edge of the village," the older man with sunglasses asked.

The blonde woman turned to the older men of the four. "Yes, these were the two humans that were found. I need a place these two to stay. Would your clans be willing to take them in for the time being?"

Both men nodded, causing the woman to smirk. "Alright then, Serena will be staying with the Aburame clan and Calem will be staying with the Akimichi clan."

Serena turned toward Calem with wide eyes. She thought back to what the woman had said before the four other men had arrived, mentally slapping herself. _How could I have been so _stupid_? Why would she leave both of us together?_

Serena latched herself onto Calem, whispering a goodbye into his ear.

Calem's arms tightened around her waist. "It'll be ok. I'll see you tomorrow, just behave," he whispered

Serena let go of Calem, giving him a weak smile before nodding.

The youngest of the hooded men walked toward Serena. "Follow me," he said before walking toward the door followed by the older man. Serena made one final glance behind her to find that Calem's hosts were now talking to him before following them toward the door.

Serena followed her hosts through the town, not quite sure what to the duo. She noticed the younger of the two stop in order to wait for Serena. Once Serena was next to him, he continued to follow the other man.

"So you know what those creatures from last night are," he asked.

"Yeah," Serena sighed, "that's why my friend and I came here. We don't want anything to happen to them."

"I see," he said.

_Sure doesn't talk much_, Serena thought to herself. "My name's Serena, Serena Fortier."

"Shino Aburame."

Before long, the trio made it to the small compound belonging to the Aburame clan. Serena followed Shino and the other man toward the house in the center of the compound. On their short trip toward the house, Serena received many looks from other members of the Aburame clan that happened to be outside.

The house wasn't the smallest that Serena had ever seen, but it sure wasn't a mansion. As she was taking her shoes off, Shino's hand brushed against Serena's shoulder as he slid past her and down the hallway. She followed him until he came to a stop in front of a small bedroom.

"You will be staying in this room. My room is across the hall if you need anything." Without another word, the boy left Serena to look around the room.

_It's not too bad, _she thought as she looked around the room. Serena flopped down onto the bed with a sigh. Staring up at the ceiling, Serena tried to think of a plan, but only succeeded in closing her eyes and sleeping through the afternoon.

**So it seems that people actually liked the first chapter of this story, so I decided to write the second one. I'm really sorry if this is a bad chapter! I've already got ideas for the next chapter and I'll start working on that tomorrow. Thank you to all of my readers! :)**


	3. Meeting the Council

**Chapter 3: Meeting the Council**

A knock at the door caused Serena to wake from her slumber. Groaning, she rubbed the sleep from her eyes and mumbled for the person to come in. She turned toward the door as Shino walked into the room. "You should get ready for the council meeting. We will be leaving in half an hour."

"Where's the bathroom," Serena asked groggily.

"It's down the hall." Shino gestured next to her bed, causing her to look down only to find her bag "a messenger brought your bag last night."

And with that, Shino left the room. Grabbing her bag, she made her way down the hall toward the bathroom. Serena knocked on the door and, receiving no answer, walked into the empty bathroom. She looked around, noticing a small shower in the corner next to a large tub.

_No time for a bath_, she thought sadly.

She reached into her bag, grabbing her toothbrush, toothpaste, and hair brush before starting the shower. After a quick shower, Serena wrapped herself in one of the towels while she quickly brushed her teeth and brushed her hair.

Throwing her brushes and toothpaste into her bag, Serena rummaged through her bag for an extra pair of clothes. She smiled as she pulled out a pair of skinny jeans and a blue, strapless top. She quickly pulled the clothes on before she pulled out a pair of boots, pulling them on as well. Looking in the mirror, Serena pulled her hair into a ponytail before throwing on a white fedora for good measure.

She walked out of the bathroom and wandered down the hall until she reached the main room. She found only Shino standing by the door. "Where's the other guy from last night?"

Shino turned to the girl, "my father has already left. He's a member of the council."

"Alright, I guess we should head over too."

Shino nodded before walking out the door. Serena sighed before following the quiet teenager. Before she knew it, Serena was led into a large room. Calem stood in the middle of the room, while the council was around the edges of the room. Serena smiled, walking up to Calem before throwing her arms around him. After a moment, she released her friend before they both turned to face the council.

"Welcome to the Council of Konohagakure," the blonde woman from yesterday, Tsunade, said.

"It's an honor to be presented to the council," Calem said, bowing to the council. Serena fought the urge to roll her eyes before following Calem's example.

A growl was heard from the door as a young man with white eyes and long haired, brunette boy. Serena's eyes widened when four of her Pokémon were dragged in, along with four of Calem's Pokémon. She glanced from the boy, to the chains that he held.

"Let them go," Serena hissed, making her way over to the brunette teen. Calem raced over to Serena, pulling her back. She whirled around to face her friend, but stopped when she saw the look on his face.

"_S'il vous plaît_ Serena," he pleaded, "don't make this worse."

The duo walked back to the center of the room, the elders watching their every move. Serena looked up to see one of the elders, a man with nearly half his face covered in bandages, watching them closely.

"So these beasts are yours," the man asked.

"They are not beasts," Serena said coldly, "they're Pokémon."

"They're a liability," the female elder said.

"How are they liability," Calem asked calmly.

"We don't have any control over these… Pokémon," Tsunade replied.

"Of course you don't," Serena scoffed, "you're not their trainer." She pointed between Calem and herself, "we are."

"So, you have complete control over these creatures," the wrapped elder asked, the revelation having piqued his interest.

Serena opened her mouth to respond, only to be cut off by Calem. "Not exactly," he said, "they have minds of their own."

"But witnesses say that you called commands and the Pokémon acted immediately," Tsunade countered.

"We've worked with our Pokémon long enough that they are willing to trust our judgment," Serena said, finally calming down somewhat.

Mumbles filled the room. Council members turned to each other, discussing the advantages of these creatures.

Clearing her throat, Tsunade waited for the council to quiet before turning toward the two teens again. "What about the larger creatures from last night? Are they Pokémon as well?"

Serena nodded, "Xerneas and Yveltal are Pokémon."

"But they're special cases," Calem finished.

"How so," Tsunade inquired.

"They're extremely rare. Very few people see them, and if you manage to capture them, breading is extremely difficult," Serena said, rubbing the back of her neck

"Didn't Ethan and Lyra find a baby Lugia and its mother," Calem said, turning to Serena.

"Yeah, that's right," Serena said, "but I still haven't figured out the conditions that-"

Tsunade cleared her throat, glancing at Serena. She shrugged before turning to Calem, mouthing the words "we'll talk later."

The council continued asking question after question until they determined that they had heard all that they needed to hear. Sending Serena and Calem out of the room, the two waited in the hall.

"Do you think we did ok," Serena asked, leaning against the wall.

"Well," Calem sighed, leaning against the opposite wall, "your attitude in the beginning didn't help us-"

"Calem, they brought our Pokémon into the room in chains, how did you think I was going to react?"

"I know Serena, but you have to keep your cool. Getting angry won't help anyone."

Serena sighed before silence fell over the two. After what seemed like an hour, Serena and Calem were called back into the council room.

"We have determined," Tsunade began, "that you may stay in the village."

Serena and Calem turned toward each other, grinning, before the female elder spoke. "However, you must provide our shinobi with these Pokémon."

"And," the wrapped elder said, a smug look on his face, "we recommend that you both marry in to one of the clans in the village."

Serena and Calem stared at the council in disbelief. Calem, being the first to recover, cleared his throat, "first of all, we don't have any extra Pokémon to give to any of your shinobi."

"And second, you can't just force us to marry someone from your village. You may be able to use your own citizens as your pawns, but we're not going to be here much longer, Arceus willing," Serena added, finally coming out of her stupor.

"We're not _forcing_ you to marry anyone," the wrapped man replied, "we're merely _suggesting_ that you marry."

"All you want to do is make sure that we're under your thumb and it's not going to happen," Serena said coldly before turning to the rest of the council. "Thank you for allowing the two of us to stay. If we do find a way to give your shinobi Pokémon, Calem and I will be the ones that will determine who will actually receive Pokémon. Now, when can we be expecting our Pokémon back?"

"They will be brought to you by the end of today at the latest," Tsunade said.

"Can we go and pick them up," Calem asked, "since I'm sure no one besides the two of us know how to use a Pokéball and your citizens would probably start to panic if they saw some of our Pokémon."

Tsunade nodded, gesturing to the brunette boy from earlier, "Neji will take you both to your other Pokémon and their capsules."

The boy, Neji, unchained the Pokémon that had been brought into the room, all of whom tackled their respective trainers as soon as they could. After a few moments, once Calem and Serena managed to stand up, the group followed Neji downstairs. The duo proceeded to collect their Pokémon before they were returned to their Pokéballs. As they walked out of the main building, Serena turned to Calem, "do you think it's possible that other Pokémon could have made it to this world?"

"I guess so. I mean, if the legendary Pokémon made it here, why couldn't more common Pokémon make it here."

Serena nodded as a comfortable silence fell over the two. As they neared the point where the two would have to split up, Calem turned toward Serena to give the girl a hug. "We'll see each other tomorrow, don't worry."

"Where did you wanna meet up," she asked.

"How about we meet here and then we figure it out from there?"

Serena smiled and nodded, "sounds good to me."

And with that, the two friends parted ways for the day.

**I hope you guys enjoyed this chapter! Let me know what you thought! And yes, more Naruto characters will be showing up within the next few chapters! : )**


End file.
